In this paper, we design a sequential system controller, which is capable of processing parallel sequence, on the basis of analysis of control specification described by Petri Net with incidence matrix. The sequential system controller consists of input conditioning unit and petri net control unit which is composed of the token control unit and firing unit. The firing unit determines the firing condition of the transfer signal on the basis of the token status of token control unit. By the proposed scheme, we can easily develop and implement the sequential system controller of automated warehousing system, automated transportation system, elevator system, and so on, as it is possible to modify control specification by changing simply the content of incidence matrix ROM and to expand easily functional capacity as the result of modular design.design.